Genetic Linkage Map Construction and QTL Mapping of Salt Tolerance Traits in Zoysiagrass (Zoysia japonica)

Guo, Hailin; Ding, Wanwen; Chen, Xuan; Zheng, Yongqi; Wang, Zhiyong; Liu, Jianxiu

doi:10.1371/journal.pone.0107249

Cited by 40 publications

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“…Salt tolerance in plant is a complicated phenomenon and many parameters have been used as indicators to evaluate its effect, including agronomic traits [ 28 ], physiological indicators [ 26 , 29 ] and phenotypic classification [ 14 ]. As an important index for plant salt tolerance, yield served as one of the phenotypic factors in the QTL analysis of salt tolerance in tomato [ 30 , 31 ] and bread wheat [ 16 ].…”

Section: Discussionmentioning

confidence: 99%

Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers

et al. 2017

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BackgroundSalt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown.ResultsTo map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462.05 cM. Plant height of mature maize cultivated in the saline field (SPH) and plant height-based salt tolerance index (ratio of plant height between saline and control fields, PHI) were used to evaluate salt tolerance of mature maize plants. A major QTL for SPH was detected on Chromosome 1 with the LOD score of 22.4, which explained 31.2% of the phenotypic variation. In addition, the major QTL conditioning PHI was also mapped at the same position on Chromosome 1, and two candidate genes involving in ion homeostasis were identified within the confidence interval of this QTL.ConclusionsThe detection of the major QTL in adult maize plant establishes the basis for the map-based cloning of genes associated with salt tolerance and provides a potential target for marker assisted selection in developing maize varieties with salt tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1090-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers

et al. 2017

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“…Such maps have been produced for zoysiagrasses based on restriction and amplified fragment length polymorphisms, simple sequence repeats (SSRs), and combinations of these markers, and the maps have been used in quantitative trait loci analyses. 4 , 6 , 7 Moreover, sequence-tagged high-density genetic maps of Z. japonica were constructed and compared with those of Oryza sativa and Sorghum bicolor , revealing a highly conserved collinearity in the gene order of these genomes. 8 In parallel with the construction of genetic maps, transcriptome analyses have been used to identify abiotic stress-related genes 9 , 10 and genes that control tissue-specific anthocyanin pigmentation in Z. japonica .…”

Section: Introductionmentioning

confidence: 99%

Sequencing and comparative analyses of the genomes of zoysiagrasses

Tanaka

Hirakawa

Kosugi

et al. 2016

DNA Res

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Zoysia is a warm-season turfgrass, which comprises 11 allotetraploid species (2n = 4x = 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession ‘Nagirizaki’ (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella ‘Wakaba’ and Z. pacifica ‘Zanpa’ were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica ‘Kyoto’, Z. japonica ‘Miyagi’ and Z. matrella ‘Chiba Fair Green’, were accumulated, and aligned against the reference genome of ‘Nagirizaki’ along with those from ‘Wakaba’ and ‘Zanpa’. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the ‘Zoysia Genome Database’ at .

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“…A stringent LOD threshold 1.5 was set to identify the putative presence of QTLs associated with economic traits of blades. A QTL was declared when the LOD value was higher than threshold of 1.5 [59]. QTLs were named and shown in italic by prepending a lower-case ‘q’ to the abbreviation of a trait name, followed by the serial number of LGs where the QTL was found and a terminal number providing a unique number to distinguish multiple QTLs of one trait on a single chromosome [60, 61], e.g.…”

Section: Methodsmentioning

confidence: 99%

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Huang

Yan

2018

Preprint

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17 Pyropia yezoensis is an important economic seaweed, to construct a genetic linkage map 18 and analyze the quantitative trait loci (QTLs) of blades, a doubled haploid (DH) 19 population containing 148 DH strains established from the intraspecific hybridization 20 between two strains with different colors was used in the present study and genotyped 21 using 79 pairs of polymorphic sequence-related amplified polymorphism (SRAP) 22 markers labeled with 5'-HEX and capillary electrophoresis. A chi-square test for 23 significance of deviations from the expected ratio (1:1) on the loci which were 24 polymorphic between parents and segregated in mapping population identified 301 loci 25 with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed 26 segregation (0.001 ≤ P < 0.01). The map was constructed using JoinMap software after a 27 total of 92 loci were assembled into three linkage groups. The map spanned 557.36 cM 28 covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM.29 Kolmogorov-Smirnov test (α=5%) of the marker positions along each LG showed a 30 uniform distribution. After that, 10 QTLs associated with five economic traits of blades 31 were detected, among which one QTL was for length, one for width, two for fresh 32 weight, two for specific growth rate of length and four for specific growth rate of fresh 33 weight. These QTLs could explain 2.29-7.87% of the trait variations, indicating that 34 their effects were all minor. The results will serve as a framework for future marker-35 assisted breeding in P. yezoensis. 36 37 Keywords: Economic trait; genetic linkage map; Pyropia yezoensis; quantitative trait 38 locus; SRAP 39 40 Introduction 41 Pyropia yezoensis is a marine red alga with high nutritional values and is one of the 42 most important maricultural crops across the world, mainly in Japan, Korea and China 43 [1]. During the cultivation of P. yezoensis, hundreds of tons of nutrients (nitrogen and 44 phosphorus) are removed by blade harvest from the eutrophic seawaters every year [2]. 45 However, some problems such as germplasm degeneration, frequent diseases and bad 46 harvests [3-5] have arisen under the influence of global warming [6]. Therefore, new 47 varieties with higher yield, stronger resistant to abiotic stress and greater ecological 48 adaptability were urgently needed for the stable development of Pyropia industry. 49 50 The traditional breeding methods of P. yezoensis are based on either observed variations 51 by selecting blades with induced variants [3, 7, 8], or controlled crosses by selecting 52 blades presenting recombination of desirable genes from different parents [9-11]. 53 However, traditional breeding is usually time-consuming and less efficient [12], and has 54 a limited ability to breed complex characters [13]. Fortunately, progress in molecular 55 genetics has enabled plant breeders the direct selection of genotypes, thereby accelerates 56 crop improvement [14]. Molecular marker-assisted selection (MAS) has become the 57 main d...

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Genetic Linkage Map Construction and QTL Mapping of Salt Tolerance Traits in Zoysiagrass (Zoysia japonica)

Cited by 40 publications

References 47 publications

Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers

Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers

Sequencing and comparative analyses of the genomes of zoysiagrasses

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

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